def launchCommand(self, cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, timeout=None, nice=0):
"""Execute a program in a new process
Args:
command: a string representing a unix command to execute
stdout: this attribute is a file object that provides output from the child process
stderr: this attribute is a file object that provides error from the child process
timeout: Number of seconds before a process is consider inactive, usefull against deadlock
nice: run cmd with an adjusted niceness, which affects process scheduling
Returns
return a 3 elements tuples representing the command execute, the standards output and the standard error message
Raises
OSError: the function trying to execute a non-existent file.
ValueError : the command line is called with invalid arguments
"""
binary = cmd.split(" ").pop(0)
if util.which(binary) is None:
self.error("Command {} not found".format(binary))
self.info("Launch {} command line...".format(binary))
self.info("Command line submit: {}".format(cmd))
(executedCmd, output, error)= util.launchCommand(cmd, stdout, stderr, timeout, nice)
if not (output is "" or output is "None" or output is None):
self.info("Output produce by {}: {} \n".format(binary, output))
if not (error is '' or error is "None" or error is None):
self.info("Error produce by {}: {}\n".format(binary, error))
self.info("------------------------\n")
def __correctionEddy(self, source, mask, topup, index, acqp, bVecs, bVals):
"""Performs eddy correction on a dwi file.
Args:
source: File containing all the images to estimate distortions for
mask: Mask to indicate brain
topup: Base name for output files from topup
index: File containing indices for all volumes in --imain into --acqp and --topup
acqp: File containing acquisition parameters
bvecs: File containing the b-vectors for all volumes in --imain
bvals: File containing the b-values for all volumes in --imain
Returns:
The resulting file name
"""
self.info("Launch eddy correction from fsl")
tmp = self.buildName(source, "tmp")
target = self.buildName(source, "eddy")
if util.which('eddy_openmp_patch'):
cmd = "eddy_openmp_patch --imain={} --mask={} --index={} --acqp={} --bvecs={} --bvals={} --out={} --data_is_shelled " \
.format(source, mask, index, acqp, bVecs, bVals, tmp)
else:
cmd = "eddy_openmp --imain={} --mask={} --index={} --acqp={} --bvecs={} --bvals={} --out={} " \
.format(source, mask, index, acqp, bVecs, bVals, tmp)
if topup is not None:
cmd += " --topup={}".format(topup)
self.getNTreadsEddy()
self.launchCommand(cmd, nice=5*60*60)
return self.rename(tmp, target)
def __correctionEddy(self, source, mask, topup, index, acqp, bVecs, bVals):
"""Performs eddy correction on a dwi file.
Args:
source: File containing all the images to estimate distortions for
mask: Mask to indicate brain
topup: Base name for output files from topup
index: File containing indices for all volumes in --imain into --acqp and --topup
acqp: File containing acquisition parameters
bvecs: File containing the b-vectors for all volumes in --imain
bvals: File containing the b-values for all volumes in --imain
Returns:
The resulting file name
"""
self.info("Launch eddy correction from fsl")
tmp = self.buildName(source, "tmp")
target = self.buildName(source, "eddy")
if util.which('eddy_openmp_patch'):
cmd = "eddy_openmp_patch --imain={} --mask={} --index={} --acqp={} --bvecs={} --bvals={} --out={} --data_is_shelled " \
.format(source, mask, index, acqp, bVecs, bVals, tmp)
else:
cmd = "eddy_openmp --imain={} --mask={} --index={} --acqp={} --bvecs={} --bvals={} --out={} " \
.format(source, mask, index, acqp, bVecs, bVals, tmp)
if topup is not None:
cmd += " --topup={}".format(topup)
self.getNTreadsEddy()
self.launchCommand(cmd, nice=5 * 60 * 60)
return self.rename(tmp, target)
def launchCommand(self,
cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
nice=0):
"""Execute a program in a new process
Args:
command: a string representing a unix command to execute
stdout: this attribute is a file object that provides output from the child process
stderr: this attribute is a file object that provides error from the child process
nice: run cmd with an adjusted niceness, which affects process scheduling
Returns
return a 3 elements tuples representing the command execute, the standards output and the standard error message
Raises
OSError: the function trying to execute a non-existent file.
ValueError : the command line is called with invalid arguments
"""
binary = cmd.split(" ").pop(0)
if util.which(binary) is None:
self.error("Command {} not found".format(binary))
self.info("Launch {} command line...\n".format(binary))
self.info("Command line submit: {}\n".format(cmd))
out = None
err = None
if stdout == 'log':
out = self.getLog()
self.info("Output will be log in {} \n".format(out.name))
if stderr == 'log':
err = self.getLog()
self.info("Error will be log in {} \n".format(err.name))
(output, error) = util.launchCommand(cmd, out, err, nice)
if stdout is not "None":
self.info("Output produce by {}: {} \n".format(binary, output))
if error != '' or error != "None":
self.info("Error produce by {}: {}\n".format(binary, error))
self.info("------------------------\n")
def launchCommand(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
timeout=None,
nice=0):
import sys
sys.path.append('/home/grg/toad')
from lib import util
"""Execute a program in a new process
Args:
command: a string representing a unix command to execute
stdout: this attribute is a file object that provides output from the child process
stderr: this attribute is a file object that provides error from the child process
timeout: Number of seconds before a process is consider inactive, usefull against deadlock
nice: run cmd with an adjusted niceness, which affects process scheduling
Returns
return a 3 elements tuples representing the command execute, the standards output and the standard error message
Raises
OSError: the function trying to execute a non-existent file.
ValueError : the command line is called with invalid arguments
"""
binary = cmd.split(" ").pop(0)
if util.which(binary) is None:
print("Command {} not found".format(binary))
print("Launch {} command line...".format(binary))
print("Command line submit: {}".format(cmd))
(executedCmd, output, error) = util.launchCommand(cmd, stdout, stderr,
timeout, nice)
if not (output is "" or output is "None" or output is None):
print("Output produce by {}: {} \n".format(binary, output))
if not (error is '' or error is "None" or error is None):
print("Error produce by {}: {}\n".format(binary, error))
dirs = '- ' + err.strerror + '\n'
for entry in listing:
absolute = os.path.join(target, entry)
if os.path.isdir(absolute):
dirs += '+ %s/\n' % entry
else:
entry = slash(entry, '\\+$-')
files += '%s\n' % entry
output = (dirs + files) or '\n'
elif sign == '-':
# dunno here
pass
elif tree:
if which('ruby'):
cmd = ['ruby', which('xiki')]
else:
cmd = ['xiki']
cmd += tree.split(' ')
if cmd:
if persist:
insert(view, edit, sel, '', indent + INDENTATION)
spawn(view, edit, indent, cmd, sel)
else:
output = communicate(cmd, None, 3, return_error=True)
if oldcwd:
os.chdir(oldcwd)
sys.path.append(
os.path.join(os.path.dirname(os.path.realpath(__file__)), '../..'))
print os.path.join(os.path.dirname(os.path.realpath(__file__)), '..')
from lib import util
__author__ = "Guillaume Valet"
__copyright__ = "Copyright (C) 2014, TOAD"
__credits__ = ["Guillaume Valet", "Mathieu Desrosiers"]
# Run this script from its own directory
cwd = os.getcwd()
if not 'toad/doc/toad' in cwd:
print "Please Run this script from its own directory, toad/doc/toad"
sys.exit()
pandoc = util.which("pandoc")
if pandoc is None:
print("pandoc not found. Please install the package")
sys.exit()
# French version
target_dir = 'src/fr/tuto/'
target_file = '../../../Toad_Tuto_fr.pdf'
header = '../../../head_tuto_fr'
tpl = '../../../../doc_latex.template'
os.chdir(target_dir)
print(os.getcwd())
cmd = "pandoc -s -S %s *.md -o %s --template=%s --number-sections" % (
header, target_file, tpl)
print cmd
os.system(cmd)
def xiki(view):
settings = view.settings()
output = None
cmd = None
oldcwd = None
if settings.get('xiki'):
indent, sign, path, tag, tree = find_tree(view)
print 'xiki', sign, path, tree
pos = get_pos(view)
if get_line(view, 1).startswith(indent + INDENTATION):
if sign == '-':
replace_line(view, pos, indent + '+ ' + tag)
edit = view.begin_edit()
cleanup(view, edit, pos, indent + INDENTATION)
select(view, pos)
view.end_edit(edit)
return
elif sign == '$':
if path:
oldcwd = os.getcwd()
# maybe this should be offloaded into find_tree
# so path will be multiple directories instead of just a base dir
path_re = r'^(.+)/%s$' % re.escape(tag)
match = re.match(path_re, tree)
if match:
os.chdir(os.path.join(path, match.group(1)))
else:
os.chdir(path)
cmd = shlex.split(tag.encode('ascii', 'replace'), True)
elif path:
# directory listing or file open
target = os.path.join(path, tree)
if os.path.isfile(target):
sublime.active_window().open_file(target)
return
elif os.path.isdir(target):
dirs = ''
files = ''
for entry in os.listdir(target):
absolute = os.path.join(target, entry)
if os.path.isdir(absolute):
dirs += '+ %s/\n' % entry
else:
files += '%s\n' % entry
output = (dirs + files) or '\n'
elif sign == '-':
# dunno here
return
elif tree:
if which('ruby'):
cmd = ['ruby', which('xiki')]
else:
cmd = ['xiki']
cmd += tree.split(' ')
if cmd:
output = communicate(cmd, None, 3, return_error=True)
if oldcwd:
os.chdir(oldcwd)
if output:
if sign == '+':
replace_line(view, pos, indent + '- ' + tag)
insert(view, output, indent + INDENTATION)
dirs = '- ' + err.strerror + '\n'
for entry in listing:
absolute = os.path.join(target, entry)
if os.path.isdir(absolute):
dirs += '+ %s/\n' % entry
else:
entry = slash(entry, '\\+$-')
files += '%s\n' % entry
output = (dirs + files) or '\n'
elif sign == '-':
# dunno here
pass
elif tree:
if which('ruby'):
cmd = ['ruby', which('xiki')]
else:
cmd = ['xiki']
cmd += tree.split(' ')
if cmd:
if persist:
insert(view, edit, sel, '', indent + INDENTATION)
spawn(view, edit, indent, cmd, sel)
else:
output = communicate(cmd, None, 3, return_error=True)
if oldcwd:
os.chdir(oldcwd)
sys.path.append(os.path.join(os.path.dirname(os.path.realpath(__file__)), '../..'))
print os.path.join(os.path.dirname(os.path.realpath(__file__)), '..')
from lib import util
__author__ = "Guillaume Valet"
__copyright__ = "Copyright (C) 2014, TOAD"
__credits__ = ["Guillaume Valet", "Mathieu Desrosiers"]
# Run this script from its own directory
cwd = os.getcwd()
if not 'toad/doc/toad' in cwd:
print "Please Run this script from its own directory, toad/doc/toad"
sys.exit()
pandoc = util.which("pandoc")
if pandoc is None:
print("pandoc not found. Please install the package")
sys.exit()
# French version
target_dir = 'src/fr/tuto/'
target_file = '../../../Toad_Tuto_fr.pdf'
header = '../../../head_tuto_fr'
tpl = '../../../../doc_latex.template'
os.chdir(target_dir)
print(os.getcwd())
cmd = "pandoc -s -S %s *.md -o %s --template=%s --number-sections" % (header, target_file, tpl)
print cmd
os.system(cmd)
